Three‐Residue Turns in α/β‐Peptides and Their Application in the Design of Tertiary Structures

A new three‐residue turn was serendipitously discovered in α/β hybrid peptides derived from alternating C‐linked carbo‐β‐amino acids (β‐Caa) and L ‐Ala residues. The three‐residue β‐α‐β turn at the C termini, nucleated by a helix at the N termini, resulted in helix‐turn (HT) supersecondary structures in these peptides. The turn in the HT motif is stabilized by two H bonds—CO(i?2)–NH(i), with a seven‐membered pseudoring (γ turn) in the backward direction, and NH(i?2)–CO(i), with a 13‐membered pseudoring in the forward direction (i being the last residue)—at the C termini. The study was extended to generalize the new three‐residue turn (β‐α‐β) by using different α‐ and β‐amino acids. Furthermore, the HT motifs were efficiently converted, by an extension with helical oligomers at the C termini, into peptides with novel helix‐turn‐helix (HTH) tertiary structures. However, this resulted in the destabilization of the β‐α‐β turn with the concomitant nucleation of another three‐residue turn, α‐β‐β, which is stabilized by 11‐ and 15‐membered bifurcated H bonds. Extensive NMR spectroscopic studies were carried out to delineate the secondary and tertiary structures in these peptides, which are further supported by molecular dynamics (MD) investigations.     

含聚碳酸酯、4-羟基苯甲酸、己二醇和1,4-苯二甲酸结构的嵌段共聚物的合成与表征

以端酰氯基团的热致液晶共聚酯ＨＴＨ ６和端酚羟基的聚碳酸酯（ＰＣ）齐聚物为原料，通过溶液缩聚法制备了含ＰＣ和ＨＴＨ ６的嵌段共聚物，并用ＩＲ、ＰＯＭ、ＤＳＣ、ＷＡＸＤ等手段对共聚物结构、热行为和结晶行为进了表征．ＤＳＣ和ＰＯＭ结果证明这些嵌段共聚物都属向列型热致性液晶．在２８０℃以下的温度范围内无相分离，而在较高温度（＞２８０℃）为两相结构．共聚物的结晶结构与ＨＴＨ ６相同，结晶度随ＨＴＨ ６含量增加而增加，结晶速度也受到ＰＣ含量的影响．     

Structure, stability, and interconversion barriers of the rotamers of cis-[Pt(II)Cl(2)(quinoline)2] and cis-[Pt(II)Cl(2)(3-bromoquinoline)(quinoline)] from X-ray crystallography, NMR spectroscopy and molecular mechanics evidence

Reported are the preparations of cis-[PtCl(2)(quinoline)(2)] and cis-[PtCl(2)(3-bromoquinoline)(quinoline)] and an investigation of the stabilities and interconversion of the rotamer forms of these complexes. Both head-to-head (HTH) and head-to-tail (HTT) rotamer forms are found in the crystal structure of cis-[PtCl(2)(quinoline)(2)]. The NOESY NMR spectrum of cis-[PtCl(2)(quinoline)(2)] in dmf-d(7) at 300 K is consistent with conformational exchange brought about by rotation about the Pt-N(quinoline) bonds. H.H nonbonded distances between H atoms of the two different quinoline ligands were determined from NOESY data, and these distances are in accord with those observed in the crystal structure and derived from molecular mechanics models. cis-[PtCl(2)(3-bromoquinoline)(quinoline)] was prepared to alleviate the symmetry-imposed absence of inter-ring H2/H2 and H8/H8 NOESY cross-peaks for cis-[PtCl(2)(quinoline)(2)]. Molecular mechanics calculations on the complexes show the HTT rotamers to be 1-2 kJ mol(-)(1) more stable than the HTH forms, consistent with the (1)H spectra where the intensities of resonances for the two forms are approximately equal. Variable-temperature (1)H NMR spectra of cis-[PtCl(2)(quinoline)(2)] in dmf-d(7) indicate a rotational energy barrier of 82 +/- 4 kJ mol(-)(1). Variable-temperature (1)H NMR spectra indicate that the Br substituent on the quinoline ring does not affect the energy barrier to interconversion between the HTT and HTH forms (79 +/- 5 kJ mol(-)(1)). The steric contribution to the rotation barrier was calculated using molecular mechanics calculations and was found to be approximately 40 kJ mol(-)(1), pointing to a possible need for an electronic component to be included in future models.     

Cytoprotective Potential of Aged Garlic Extract (AGE) and Its Active Constituent,S-allyl-l-cysteine,in Presence of Carvedilol during Isoproterenol-Induced Myocardial Disturbance and Metabolic Derangements in Rats

This study was conducted to determine the potential interaction of aged garlic extract (AGE) with carvedilol (CAR), as well as to investigate the role of S-allyl-l-cysteine (SAC), an active constituent of AGE, in rats with isoproterenol (ISO)-induced myocardial dysfunction. At the end of three weeks of treatment with AGE (2 and 5 mL/kg) or SAC (13.1 and 32.76 mg/kg), either alone or along with CAR (10 mg/kg) in the respective groups of animals, ISO was administered subcutaneously to induce myocardial damage. Myocardial infarction (MI) diagnostic predictor enzymes, lactate dehydrogenase (LDH) and creatinine kinase (CK-MB), were measured in both serum and heart tissue homogenates (HTH). Superoxide dismutase (SOD), catalase, and thiobarbituric acid reactive species (TBARS) were estimated in HTH. When compared with other groups, the combined therapy of high doses of AGE and SAC given alone or together with CAR caused a significant decrease in serum LDH and CK-MB activities. Further, significant rise in the LDH and CK-MB activities in HTH was noticed in the combined groups of AGE and SAC with CAR. It was also observed that both doses of AGE and SAC significantly increased endogenous antioxidants in HTH. Furthermore, histopathological observations corroborated the biochemical findings. The cytoprotective potential of SAC and AGE were dose-dependent, and SAC was more potent than AGE. The protection offered by aged garlic may be attributed to SAC. Overall, the results indicated that a high dose of AGE and its constituent SAC, when combined with carvedilol, has a synergistic effect in preventing morphological and physiological changes in the myocardium during ISO-induced myocardial damage.     

Design and Enantioselective Synthesis of a Peptidomimetic of the Turn in the Helix-Turn-Helix DNA-Binding Protein Motif

A peptidomimetic of the turn in the helix-turn-helix (HTH) motif of DNA-binding proteins was designed and synthesized. Conformational constraint was achieved by an unusual linking of two amino acids with a side chain carbon-carbon bond. A phenyl ring provides the potential for new hydrophobic contacts with the hydrophobic core of the HTH motif. In the mimic, the peptide backbone and the central residue were retained in native form within a 12-membered cyclic tripeptide. The target compound 1b was synthesized by two sequential Horner-Wittig couplings followed by enantioselective hydrogenation with Rh(MeDuPHOS) in eight steps and 35% overall yield. The stereochemical outcome of the key hydrogenation was determined by aromatic ring oxidation with RuO(2)/NaIO(4) to give 2 equiv of Boc-Asp-OMe.     

Supersecondary structure prediction using Chou's pseudo amino acid composition

Supersecondary structures (SSSs) are the building blocks of protein 3D structures. Accurate prediction of SSSs can be one important step toward building a tertiary structure from the specified secondary structure. How to improve the accuracy of prediction of SSSs by effectively incorporating the sequence order effects is an important and challenging problem. Based on a different form of Chou's pseudo amino acid composition, a novel approach for feature representation of SSSs is proposed. Amino acid basic compositions, dipeptide components, and amino acid composition distribution are incorporated to represent the compositional features of proteins. Each supersecondary structural motif is characterized as a vector of 36 dimensions. In addition, we propose a novel prediction system by using SVM and IDQD algorithm as classifiers. Our method is trained and tested on ArchDB40 dataset containing 3088 proteins. The highest overall accuracy for the training dataset and the independent testing dataset are 77.7 and 69.4%, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Design of peptide that recognizes double-stranded DNA.

A novel molecular tool for double-stranded (ds) DNA detection using synthetic peptide is described. The peptide was designed based on the DNA binding domain of the lambda phage CRO repressor (CRO). The designed peptides contain helix-turn-helix (HTH), which is DNA binding motif. A cyclic peptide and a mutant peptide based on CRO were also designed, and the resulting affinity for dsDNA was increased. Furthermore, native amino acids of the peptide were replaced with arginine to increase the affinity for dsDNA. The affinity of these peptides for DNA binding was assessed by surface plasmon resonance (SPR) technique.     

Predicting helical hairpins from sequences by Monte Carlo simulations

The key problem in polypeptide‐structure prediction is with regard to thermodynamics. Two factors limit prediction in ab initio computer simulations. First, the thermodynamically dominant conformations must be found from an extremely large number of possible conformations. Second, these low‐energy forms must deviate little from the experimental structures. Here, we report on the application of the diffusion‐controlled Monte Carlo approach to predict four α‐helical hairpins with 34–38 residues by global optimization, using an energy optimized on other supersecondary structures. A total of seven simulations is carried out for each protein starting from fully extended conformations. Three proteins are correctly folded (within 3.0 Å rms from the experimental structures), but the fourth protein cannot distinguish between several equienergetic conformations. Possible improvement of the energy model is suggested. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 582–589, 2000     

Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k

Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1-43) and EF2 (residues 44-75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitro experiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutated calbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 A with respect to the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independent in silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, that is, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2 homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linear correlations between thermodynamic data and ZDOCK scores were built, providing a tested tool for very fast in silico predictions of the free energy of association of protein-protein complexes solved at the atomic level and known to not undergo significant conformational changes upon binding.     

Engineering a β‐Helical d,l‐Peptide for Folding in Polar Media

β Helices—helices formed by alternating d,l ‐peptides and stabilized by β‐sheet hydrogen bonding—are found naturally in only a handful of highly hydrophobic peptides. This paper explores the scope of β‐helical structure by presenting the first design and biophysical characterization of a hydrophilic d,l ‐peptide, 1 , that forms a β helix in methanol. The design of 1 is based on the β‐hairpin/β helix—a new supersecondary that had been characterized previously only for hydrophobic peptides in nonpolar solvents. Incorporating polar residues in 1 provided solubility in methanol, in which the peptide adopts the expected β‐hairpin/β‐helical structure, as evidenced by CD, analytical ultracentrifugation (AUC), NMR spectroscopy, and NMR‐based structure calculations. Upon titration with water (at constant peptide concentration), the structure in methanol ( 1 m ) transitions cooperatively to an extended conformation ( 1 w ) resembling a cyclic β‐hairpin; observation of an isodichroic point in the solvent‐dependent CD spectra indicates that this transition is a two‐state process. In contrast, neither 1 m nor 1 w show cooperative thermal melting; instead, their structures appear intact at temperatures as high as 65 °C; this observation suggests that steric constraint is dominant in stabilizing these structures. Finally, the ¹H NMR CαH spectroscopic resonances of 1 m are downfield‐shifted with respect to random‐coil values, a hitherto unreported property for β helices that appears to be a general feature of these structures. These results show for the first time that an appropriately designed β‐helical peptide can fold stably in a polar solvent; furthermore, the structural and spectroscopic data reported should prove useful in the future design and characterization of water‐soluble β helices.     

Dynamic x-ray diffraction studies of liquid-crystalline polyesters

Mesophase transitions in liquid-crystalline (LC) polyesters were studied by dynamic x-ray diffraction using a synchrotron radiation source. Powder and fiber samples were examined by continuous heating from 50°C to 270°C in a hot stage. The polymer systems consisted of two types of thermotropic polyesters with mesogenic cores composed of combinations of substituted terephthalate, oxybenzoate and hydroquinone units combined with aliphatic spacers placed in the main chain. One of these samples was a chemically homogeneous LC polyester (HTH12) while the other LC polyester possessed chemical heterogeneity (BP6). BP6 could also be processed to form fibers which showed thermal transition behavior by x-ray diffraction and no detectable melting or clearing transition by thermal measurements. LC textures were observed using polarized light microscopy. Results of the dynamic x-ray diffraction studies of these two LC polymers are described.     

Thermal decomposition mechanisms of sequential bipolyesters based on propeneglycol and hydroxybenzoic/phthalic diacid derivatives

Some bipolyesters consisting of 1,2-propene glycol residue (P) and symmetric aromatic diacid residue constituted by two p-oxybenzoyl groups coupled by a terephthaloyl (HTH), phthaloyl (HOH) and isophthaloyl (HIH) group, and a nonsymmetric diacid residue constituted by a p-oxybenzoyl and a terephthaloyl group (HT), have been investigated by direct pyrolysis–mass spectrometry. The results show that intramolecular exchange reactions occurring at the pyrolysis stage cause a reorganization of the copolymer sequences. Sequential bipolyesters I–IV are ideal materials for the investigation of the extent of thermal reorganization induced in the bipolymer sequences by the pyrolytic process.     

Synthesis of new 1,2-dideoxy C-linked carbo-β-amino acids and α/β-peptides with 11/9-helix,helix-turn and helix-turn-helix structures

The present study describes the synthesis of new C-linked carbo-β-amino acids [β-Caa_(1,2-ddx)], with a 1,2-dideoxy D-xylo furanoside side chain (a tetrahydro furan derivative). The stereochemistry at the newly created amine centers was determined by modified Mosher method. The (S)-β-Caa_(1,2-ddx) prepared from d-mannose diacetonide were utilized for the synthesis of 1:1 α/β-peptides with L-Ala. The conformational analysis (NMR, MD and CD) revealed the presence of 11/9-helix, helix induced helix-turn (HT) and helix-turn-helix (HTH) in these peptides. These side chains with tetrahydrofuran ring facilitated the formation of robust helix, unlike some other side chains from earlier studies.     

De novo and inverse folding predictions of protein structure and dynamics

Summary In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 ? from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem.     

Mass spectrometric study of thermal desorption of water from surface of titanosilica

A study has been made of the thermal desorption of water from the surface of titanosilica (TS) obtained by high-temperature hydrolysis (HTH) and low-temperature hydrolysis (LTE), and containing up to 37% TiO₂ by weight. For the samples of TS obtained by either method, only one thermal desorption maximum is observed; the position of the maximum does not depend on the content of the titanium dioxide phase in the TS, but it does depend on the method of preparation: For the LTH, T_max = 480 K; and for the ETH, T_max = 400 K. The shift of the temperature corresponding to the maximum of the H₂O⁺ desorption peak for the TS obtained by HTH may be due to migration of adsorbed water molecules along the surface to sections of titanium-siloxane bonds Si-O-Ti, from which the water molecules are then desorbed.Institute of Surface Chemistry, Ukrainian Academy of Sciences, Kiev. Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 27, No. 6, pp. 734–736, November–December, 1991. Original article submitted February 20, 1989.     

Sequence-selective DNA cleavage by a chimeric metallopeptide

A chimeric metallopeptide derived from the sequences of two structurally superimposable motifs was designed as an artificial nuclease. Both DNA recognition and nuclease activity have been incorporated into a small peptide sequence. P3W, a 33-mer peptide comprising helices alpha2 and alpha3 from the engrailed homeodomain and the consensus EF-hand Ca-binding loop binds one equivalent of lanthanides or calcium and folds upon metal binding. The conditional formation constants (in the presence of 50 mM Tris) of P3W for Eu(III) (K(a) = (2.1 +/- 0.1) x 10(5) M(-1)) and Ce(IV) (K(a) = (2.6 +/- 0.1) x 10(5) M(-1)) are typical of isolated EF-hand peptides. Circular dichroism studies show that 1:1 CeP3W is 26% alpha-helical and EuP3W is up to 40% alpha-helical in the presence of excess metal. The predicted helicity of the folded peptide based on helix length and end effects is about 50%, showing the metallopeptides are significantly folded. EuP3W has considerably more secondary structure than our previously reported chimeras (Welch, J. T.; Sirish, M.; Lindstrom, K. M.; Franklin, S. J. Inorg. Chem. 2001, 40, 1982-1984). Eu(III)P3W and Ce(IV)P3W nick supercoiled DNA at pH 6.9, although EuP3W is more active at pH 8. CeP3W cleaves linearized, duplex DNA as well as supercoiled plasmid. The cleavage of a 5'-(32)P-labeled 121-mer DNA fragment was followed by polyacrylamide gel electrophoresis. The cleavage products are 3'-OPO(3) termini exclusively, suggesting a regioselective or multistep mechanism. In contrast, uncomplexed Ce(IV) and Eu(III) ions produce both 3'-OPO(3) and 3'-OH, and no evidence of 4'-oxidative cleavage termini with either metal. The complementary 3'-(32)P-labeled oligonucleotide experiment also showed both 5'-OPO(3) and 5'-OH termini were produced by the free ions, whereas CeP3W produces only 5'-OPO(3) termini. In addition to apparent regioselectivity, the metallopeptides cut DNA with modest sequence discrimination, which suggests that the HTH motif binds DNA as a folded domain and thus cleaves selected sequences. The de novo artificial nuclease LnP3W represents the first small, underivatized peptide that is both active as a nuclease and sequence selective.     

一种高可溶、高光学透明含氟聚酰亚胺的合成与表征

由自制芳香二胺单体9,9-双(3,5-二氟-4-胺基苯基)芴和商品化二酐单体4,4'-(六氟异丙基)双邻苯二甲酸酐经一步法高温缩聚制备了一种新型含氟聚酰亚胺.分别用FT-IR、1HNMR和19FNMR对所制聚酰亚胺结构进行了表征.结果证实其与所设计的结构完全一致,并且酰亚胺化反应完全.该含氟聚酰亚胺表现出高的溶解性:室温下在N-甲基-2-吡咯烷酮、N,N-二甲基乙酰胺、N,N-二甲基甲酰胺、氯仿、二氯甲烷、四氢呋喃等常规溶剂中的溶解度可达10wt%以上.由该聚酰亚胺溶液所制的薄膜无色透明,截断波长在315nm,400nm波长后的透光率在84%以上.此外该含氟聚酰亚胺还表现出良好的热学性能和机械性能:玻璃化转变温度在377℃,空气和氮气中10%热失重温度均在539℃以上;其薄膜的拉伸强度在70～80MPa,断裂伸长率在4%～8%,起始模量为2.6GPa.